Light detection devices with protective liner and methods related to same

ABSTRACT

Light detection devices and related methods are provided. The devices may comprise a reaction structure for containing a reaction solution with a relatively high or low pH and a plurality of reaction sites that generate light emissions. The devices may comprise a device base comprising a plurality of light sensors, device circuitry coupled to the light sensors, and a plurality of light guides that block excitation light but permit the light emissions to pass to a light sensor. The device base may also include a shield layer extending about each light guide between each light guide and the device circuitry, and a protection layer that is chemically inert with respect to the reaction solution extending about each light guide between each light guide and the shield layer. The protection layer prevents reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry.

CROSS-REFERENCE TO RELATED APPLICATIONS

This present application is a continuation of U.S. patent applicationSer. No. 18/145,105, filed Dec. 22, 2022, and entitled Light DetectionDevices With Protective Liner and Methods Related to Same, which is acontinuation of U.S. patent application Ser. No. 17/190,094, now U.S.Pat. No. 11,543,352, filed Mar. 2, 2021, and entitled Light DetectionDevices With Protective Liner and Methods Related to Same, which is acontinuation of U.S. patent application Ser. No. 16/216,014, now U.S.Pat. No. 10,955,343, filed Dec. 11, 2018, and entitled Light DetectionDevices With Protective Liner and Methods Related to Same, which claimspriority to U.S. Provisional Patent Application No. 62/609,889, filedDec. 22, 2017, and entitled Light Detection Devices with ProtectiveLiner and Methods of Manufacturing Same, and Dutch Application No.2020612, filed on Mar. 19, 2018, and entitled Light Detection Deviceswith Protective Liner and Methods of Manufacturing Same. The entirecontents of each of the aforementioned applications are herebyincorporated herein by reference.

BACKGROUND

Various protocols in biological or chemical research involve performinga large number of controlled reactions on local support surfaces orwithin predefined reaction chambers. The designated reactions may thenbe observed or detected and subsequent analysis may help identify orreveal properties of substances involved in the reaction. For example,in some multiplex assays, an unknown analyte having an identifiablelabel (e.g., fluorescent label) may be exposed to thousands of knownprobes under controlled conditions. Each known probe may be depositedinto a corresponding well of a microplate. Observing any chemicalreactions that occur between the known probes and the unknown analytewithin the wells may help identify or reveal properties of the analyte.Other examples of such protocols include known DNA sequencing processes,such as sequencing-by-synthesis (SBS) or cyclic-array sequencing.

In some conventional fluorescent-detection protocols, an optical systemis used to direct an excitation light onto fluorescently-labeledanalytes and to also detect the fluorescent signals that may be emittedfrom the analytes. However, such optical systems can be relativelyexpensive and involve a relatively large benchtop footprint. Forexample, such optical systems may include an arrangement of lenses,filters, and light sources.

In other proposed detection systems, the controlled reactions occur onlocal support surfaces or within predefined reaction chambers providedover an electronic solid-state light detector or imager (e.g., acomplementary metal-oxide-semiconductor (CMOS) detector or acharged-coupled device (CCD) detector) that does not involve a largeoptical assembly to detect the fluorescent emissions. However, suchproposed solid-state imaging systems may have some limitations. Forexample, fluidically delivering reagents (e.g., fluorescently-labeledmolecules) in a solution to the analytes that are located on theelectronic device of such systems may present challenges. In somescenarios, the reagent solution may breach the electronic device andcorrode or otherwise deteriorate components thereof, for example.

BRIEF DESCRIPTION

In one aspect of the present disclosure, a device is provided. Thedevice comprises a reaction structure that forms a plurality of reactionrecesses for containing a reaction solution with a pH of less than orequal to about 5 or a pH greater than or equal to about 8 and at leastone reaction site that generates light emissions in response to incidentexcitation light after treatment with the reaction solution. The devicealso comprises a device base positioned beneath the reaction structure.The device base comprises a plurality of light sensors, and devicecircuitry electrically coupled to the light sensors to transmit datasignals based on photons detected by the light sensors. The device basealso comprises a plurality of light guides with input regions thatreceive the excitation light and the light emissions from at least onecorresponding reaction recess, the light guides extending into thedevice base from the input regions toward at least one correspondinglight sensor and comprising at least one filter material that filtersthe excitation light and permits the light emissions to pass to the atleast one corresponding light sensor. The device further comprises ashield layer extending about each light guide and positioned betweeneach light guide and the device circuitry. The device base alsocomprises a protection layer extending about each light guide andpositioned between each light guide and the shield layer that preventsreaction solution that passes through the reaction structure and thelight guide from interacting with the device circuitry. The protectionlayer is chemically inert with respect to the reaction solution.

In some examples, the protection layer abuts the plurality of lightguides within the device base. In some such examples, the devicecircuitry is provided within dielectric material layers of the devicebase, the shield layer is positioned between the protection layer andthe dielectric material layers, and the shield layer abuts thedielectric material layers.

In some examples, the protection layer further extends between a topsurface of the device base and interstitial areas of the reactionstructure that extend about the reaction recesses. In some suchexamples, the shield layer extends between the protection layer and thetop surface of the device base.

In some examples, the protection layer comprises silicon dioxide, ametal oxide, a metal nitride or a combination thereof. In some examples,the protection layer comprises silicon dioxide, silicon oxynitride,silicon monoxide, silicon carbide, silicon oxycarbide, siliconnitrocarbide, metal oxide, metal nitride or a combination thereof. Insome such examples, the pH of the reaction solution is greater than orequal to about 8. In some examples, the pH of the reaction solution isless than or equal to about 5, and the protection layer comprisessilicon carbide, silicon oxycarbide, silicon nitrocarbide, a metaloxide, a metal nitride or a combination thereof. In some examples, theprotection layer comprises a liquid impervious barrier layer. In someexamples, the shield layer comprises a silicon nitride shield layer.

In some examples, the device circuitry comprises interconnectedconductive elements, and the protection layer prevents the reactionsolution from oxidizing the conductive elements. In some examples, thethickness of the protection layer is within the range of about 5nanometers to about 100 nanometers. In some examples, the reactionstructure comprises at least one reaction site immobilized to thereaction structure within each of the plurality of reaction recesses,and the reaction solution may initiate a reaction and/or form a reactionproduct with the at the at least one reaction site that generates lightemissions in response to the incident excitation light. In some suchexamples, the at least one reaction site comprises at least one analyte,and the reaction solution comprises at least one fluorescently-labeledmolecule.

In some examples, the device circuitry of the device base formscomplementary metal-oxide semiconductor (CMOS) circuits.

In another aspect of the present disclosure, a biosensor is provided.The biosensor comprises any one of the devices described above. Thebiosensor also comprises a flow cell mounted to the device. The flowcell comprises the reaction solution and at least one flow channel thatis in fluid communication with the plurality of reaction recesses of thereaction structure to direct the reaction solution thereto.

In another aspect of the present disclosure, a method is provided. Themethod comprises forming a plurality of trenches within a device basecomprising a plurality of light sensors and device circuitryelectrically coupled to the light sensors to transmit data signals basedon photons detected by the light sensors, the plurality of trenchesextending from a top surface of the device base and toward at least onecorresponding light sensor. The method also comprises depositing ashield layer over the device base such that the shield layer extends atleast within the plurality of trenches, and depositing a protectionlayer over the shield layer such that the protection layer extends atleast within the plurality of trenches. The method further comprisesfilling the plurality of trenches over the deposited protection layerwith at least one filter material to form a plurality of light guides,the at least one filter material filters light of at least a firstwavelength and permits light of a second wavelength to pass therethroughto the at least one corresponding light sensor. The method alsocomprises forming a reaction structure over the plurality of lightguides and the protection layer, the reaction structure forming aplurality of reaction recesses corresponding to at least one light guidefor containing a reaction solution with a pH of less than or equal toabout 5 or a pH greater than or equal to about 8 and at least onereaction site that generates light emissions of the second wavelength inresponse to incident excitation light of the first wavelength aftertreatment with the reaction solution. The protection layer is chemicallyinert with respect to the reaction solution.

In some examples, the protection layer comprises silicon dioxide,silicon oxynitride, silicon monoxide, silicon carbide, siliconoxycarbide, silicon nitrocarbide, silicon dioxide, metal oxide, metalnitride or a combination thereof, and wherein the shield layer comprisesa silicon nitride shield layer. In some examples, depositing the shieldlayer over the device base further comprises depositing the shield layerover the top surface of the device base, and depositing the protectionlayer over the device base further comprises depositing the protectionlayer over the portion of the shield layer extending over the topsurface of the device base.

In some examples, the method further comprises passing the reactionsolution with a pH of less than or equal to about 5 or a pH greater thanor equal to about 8 over the reaction structure.

It should be appreciated that all combinations of the foregoing aspectsand additional concepts discussed in greater detail below (provided suchconcepts are not mutually inconsistent) are contemplated as being partof the inventive subject matter disclosed herein.

These and other objects, features and advantages of this disclosure willbecome apparent from the following detailed description of the variousaspects of the disclosure taken in conjunction with the accompanyingdrawings.

BRIEF DESCRIPTION OF DRAWINGS

These and other features, aspects, and advantages of the presentdisclosure will become better understood when the following detaileddescription is read with reference to the accompanying drawings, whichare not necessarily drawn to scale and in which like reference numeralsrepresent like aspects throughout the drawings, wherein:

FIG. 1 illustrates, in one example, a cross-section of a biosensor inaccordance with the present disclosure.

FIG. 2 illustrates, in one example, a top view of a detection device ofthe biosensor of FIG. 1 .

FIG. 3 illustrates, in one example, a cross-section of a portion of thedetection device of FIG. 2 illustrating a portion of a reactionstructure and a light guide thereof.

FIG. 4 illustrates, in one example, an enlarged portion of thecross-section of FIG. 3 .

FIG. 5 illustrates, in one example, the enlarged portion of thecross-section of FIG. 4 with reaction solution on the reactionstructure.

FIG. 6 illustrates, in one example, the enlarged portion of thecross-section of FIG. 4 during a light detection event.

FIG. 7 illustrates, in one example, the enlarged portion of thecross-section of FIG. 4 with discontinuities in the reaction structureand the light guide.

FIG. 8 illustrates, in one example, an enlarged portion of thecross-section of FIG. 7 with discontinuities in the reaction structure,the light guide and a shield layer thereof.

FIG. 9 is a flowchart illustrating, in one example, a method ofmanufacturing a light detection device in accordance with the presentdisclosure.

FIG. 10 illustrates, in one example, the formation of a trench in adevice base of a light detection device.

FIG. 11 illustrates, in one example, the formation of a shield layerwithin the trench in the device base of FIG. 10 .

FIG. 12 illustrates, in one example, the formation of a protection layerover the shield layer of FIG. 11 .

FIG. 13 illustrates, in one example, the formation of a light guide witha first filter material over the protection layer FIG. 12 .

DETAILED DESCRIPTION

Aspects of the present disclosure and certain examples, features,advantages, and details thereof, are explained more fully below withreference to the non-limiting examples illustrated in the accompanyingdrawings. Descriptions of well-known materials, fabrication tools,processing techniques, etc., are omitted so as not to unnecessarilyobscure the relevant details. It should be understood, however, that thedetailed description and the specific examples, while indicating aspectsof the disclosure, are given by way of illustration only, and are not byway of limitation. Various substitutions, modifications, additions,and/or arrangements, within the spirit and/or scope of the underlyinginventive concepts will be apparent to those skilled in the art fromthis disclosure.

Approximating language, as used herein throughout disclosure, may beapplied to modify any quantitative representation that could permissiblyvary without resulting in a change in the basic function to which it isrelated. Accordingly, a value modified by a term or terms, such as“about” or “substantially,” is not limited to the precise valuespecified. For example, these terms can refer to less than or equal to±5%, such as less than or equal to ±2%, such as less than or equal to±1%, such as less than or equal to ±0.5%, such as less than or equal to±0.2%, such as less than or equal to ±0.1%, such as less than or equalto ±0.05%. In some instances, the approximating language may correspondto the precision of an instrument for measuring the value.

Terminology used herein is for the purpose of describing particularexamples only and is not intended to be limiting. As used herein, thesingular forms “a”, “an” and “the” are intended to include the pluralforms as well, unless the context clearly indicates otherwise.Furthermore, references to an “example” are not intended to beinterpreted as excluding the existence of additional examples that alsoincorporate the recited features. Moreover, unless explicitly stated tothe contrary, the terms “comprising” (and any form of “comprise,” suchas “comprises” and “comprising”), “have” (and any form of “have,” suchas “has” and “having”), “include” (and any form of “include,” such as“includes” and “including”), and “contain” (and any form of “contain,”such as “contains” and “containing”) are used as open-ended linkingverbs. As a result, any examples that “comprises,” “has,” “includes” or“contains” one or more step or element possesses such one or more stepor element, but is not limited to possessing only such one or more stepor element. As used herein, the terms “may” and “may be” indicate apossibility of an occurrence within a set of circumstances; a possessionof a specified property, characteristic or function; and/or qualifyanother verb by expressing one or more of an ability, capability, orpossibility associated with the qualified verb. Accordingly, usage of“may” and “may be” indicates that a modified term is apparentlyappropriate, capable, or suitable for an indicated capacity, function,or usage, while taking into account that in some circumstances themodified term may sometimes not be appropriate, capable or suitable. Forexample, in some circumstances, an event or capacity can be expected,while in other circumstances the event or capacity cannot occur—thisdistinction is captured by the terms “may” and “may be.”

Examples described herein may be used in various biological or chemicalprocesses and systems for academic or commercial analysis. Morespecifically, examples described herein may be used in various processesand systems where it is desired to detect an event, property, quality,or characteristic that is indicative of a designated reaction. Forexample, examples described herein include light detection devices,biosensors, and their components, as well as bioassay systems thatoperate with biosensors. In some examples, the devices, biosensors andsystems may include a flow cell and one or more light sensors that arecoupled together (removably or fixedly) in a substantially unitarystructure.

The devices, biosensors and bioassay systems may be configured toperform a plurality of designated reactions that may be detectedindividually or collectively. The devices, biosensors and bioassaysystems may be configured to perform numerous cycles in which theplurality of designated reactions occurs in parallel. For example, thedevices, biosensors and bioassay systems may be used to sequence a densearray of DNA features through iterative cycles of enzymatic manipulationand light or image detection/acquisition. As such, the devices,biosensors and bioassay systems (e.g., via one or more cartridges) mayinclude one or more microfluidic channel that delivers reagents or otherreaction components in a reaction solution to a reaction site of thedevices, biosensors and bioassay systems. In some examples, the reactionsolution may be substantially acidic, such as comprising a pH of lessthan or equal to about 5, or less than or equal to about 4, or less thanor equal to about 3. In some other examples, the reaction solution maybe substantially alkaline/basic, such as comprising a pH of greater thanor equal to about 8, or greater than or equal to about 9, or greaterthan or equal to about 10. As used herein, the term “acidity” andgrammatical variants thereof refer to a pH value of less than about 7,and the terms “basicity,” “alkalinity” and grammatical variants thereofrefer to a pH value of greater than about 7.

In some examples, the reaction sites are provided or spaced apart in apredetermined manner, such as in a uniform or repeating pattern. In someother examples, the reaction sites are randomly distributed. Each of thereaction sites may be associated with one or more light guides and oneor more light sensors that detect light from the associated reactionsite. In some examples, the reaction sites are located in reactionrecesses or chambers, which may at least partially compartmentalize thedesignated reactions therein.

As used herein, a “designated reaction” includes a change in at leastone of a chemical, electrical, physical, or optical property (orquality) of a chemical or biological substance of interest, such as ananalyte-of-interest. In particular examples, a designated reaction is apositive binding event, such as incorporation of a fluorescently labeledbiomolecule with an analyte-of-interest, for example. More generally, adesignated reaction may be a chemical transformation, chemical change,or chemical interaction. A designated reaction may also be a change inelectrical properties. In particular examples, a designated reactionincludes the incorporation of a fluorescently-labeled molecule with ananalyte. The analyte may be an oligonucleotide and thefluorescently-labeled molecule may be a nucleotide. A designatedreaction may be detected when an excitation light is directed toward theoligonucleotide having the labeled nucleotide, and the fluorophore emitsa detectable fluorescent signal. In alternative examples, the detectedfluorescence is a result of chemiluminescence or bioluminescence. Adesignated reaction may also increase fluorescence (or Förster)resonance energy transfer (FRET), for example, by bringing a donorfluorophore in proximity to an acceptor fluorophore, decrease FRET byseparating donor and acceptor fluorophores, increase fluorescence byseparating a quencher from a fluorophore, or decrease fluorescence byco-locating a quencher and fluorophore.

As used herein, a “reaction solution,” “reaction component” or“reactant” includes any substance that may be used to obtain at leastone designated reaction. For example, potential reaction componentsinclude reagents, enzymes, samples, other biomolecules, and buffersolutions, for example. The reaction components may be delivered to areaction site in a solution and/or immobilized at a reaction site. Thereaction components may interact directly or indirectly with anothersubstance, such as an analyte-of-interest immobilized at a reactionsite. As noted above, the reaction solution may be substantially acidic(i.e., include a relatively high acidity) (e.g., comprising a pH of lessthan or equal to about 5, a pH less than or equal to about 4, or a pHless than or equal to about 3) or substantially alkaline/basic (i.e.,include a relatively high alkalinity/basicity) (e.g., comprising a pH ofgreater than or equal to about 8, a pH of greater than or equal to about9, or a pH of greater than or equal to about 10).

As used herein, the term “reaction site” is a localized region where atleast one designated reaction may occur. A reaction site may includesupport surfaces of a reaction structure or substrate where a substancemay be immobilized thereon. For example, a reaction site may include asurface of a reaction structure (which may be positioned in a channel ofa flow cell) that has a reaction component thereon, such as a colony ofnucleic acids thereon. In some such examples, the nucleic acids in thecolony have the same sequence, being for example, clonal copies of asingle stranded or double stranded template. However, in some examples areaction site may contain only a single nucleic acid molecule, forexample, in a single stranded or double stranded form.

A plurality of reaction sites may be randomly distributed along thereaction structure or arranged in a predetermined manner (e.g.,side-by-side in a matrix, such as in microarrays). A reaction site canalso include a reaction chamber or recess that at least partiallydefines a spatial region or volume configured to compartmentalize thedesignated reaction. As used herein, the term “reaction chamber” or“reaction recess” includes a defined spatial region of the supportstructure (which is often in fluid communication with a flow channel). Areaction recess may be at least partially separated from the surroundingenvironment other or spatial regions. For example, a plurality ofreaction recesses may be separated from each other by shared walls, suchas a detector surface. As a more specific example, the reaction recessesmay be nanowells comprising an indent, pit, well, groove, cavity ordepression defined by interior surfaces of a detection surface and havean opening or aperture (i.e., be open-sided) so that the nanowells canbe in fluid communication with a flow channel.

In some examples, the reaction recesses of the reaction structure aresized and shaped relative to solids (including semi-solids) so that thesolids may be inserted, fully or partially, therein. For example, thereaction recesses may be sized and shaped to accommodate a capture bead.The capture bead may have clonally amplified DNA or other substancesthereon. Alternatively, the reaction recesses may be sized and shaped toreceive an approximate number of beads or solid substrates. As anotherexample, the reaction recesses may be filled with a porous gel orsubstance that is configured to control diffusion or filter fluids orsolutions that may flow into the reaction recesses.

In some examples, light sensors (e.g., photodiodes) are associated withcorresponding reaction sites. A light sensor that is associated with areaction site is configured to detect light emissions from theassociated reaction site via at least one light guide when a designatedreaction has occurred at the associated reaction site. In some cases, aplurality of light sensors (e.g. several pixels of a light detection orcamera device) may be associated with a single reaction site. In othercases, a single light sensor (e.g. a single pixel) may be associatedwith a single reaction site or with a group of reaction sites. The lightsensor, the reaction site, and other features of the biosensor may beconfigured so that at least some of the light is directly detected bythe light sensor without being reflected.

As used herein, a “biological or chemical substance” includesbiomolecules, samples-of-interest, analytes-of-interest, and otherchemical compound(s). A biological or chemical substance may be used todetect, identify, or analyze other chemical compound(s), or function asintermediaries to study or analyze other chemical compound(s). Inparticular examples, the biological or chemical substances include abiomolecule. As used herein, a “biomolecule” includes at least one of abiopolymer, nucleoside, nucleic acid, polynucleotide, oligonucleotide,protein, enzyme, polypeptide, antibody, antigen, ligand, receptor,polysaccharide, carbohydrate, polyphosphate, cell, tissue, organism, orfragment thereof or any other biologically active chemical compound(s)such as analogs or mimetics of the aforementioned species. In a furtherexample, a biological or chemical substance or a biomolecule includes anenzyme or reagent used in a coupled reaction to detect the product ofanother reaction such as an enzyme or reagent, such as an enzyme orreagent used to detect pyrophosphate in a pyrosequencing reaction.Enzymes and reagents useful for pyrophosphate detection are described,for example, in U.S. Patent Publication No. 2005/0244870 A1, which isincorporated by reference in its entirety.

Biomolecules, samples, and biological or chemical substances may benaturally occurring or synthetic and may be suspended in a solution ormixture within a reaction recess or region. Biomolecules, samples, andbiological or chemical substances may also be bound to a solid phase orgel material. Biomolecules, samples, and biological or chemicalsubstances may also include a pharmaceutical composition. In some cases,biomolecules, samples, and biological or chemical substances of interestmay be referred to as targets, probes, or analytes.

As used herein, a “biosensor” includes a device that includes a reactionstructure with a plurality of reaction sites that is configured todetect designated reactions that occur at or proximate to the reactionsites. A biosensor may include a solid-state light detection or“imaging” device (e.g., CCD or CMOS light detection device) and,optionally, a flow cell mounted thereto. The flow cell may include atleast one flow channel that is in fluid communication with the reactionsites. As one specific example, the biosensor is configured tofluidically and electrically couple to a bioassay system. The bioassaysystem may deliver a reaction solution to the reaction sites accordingto a predetermined protocol (e.g., sequencing-by-synthesis) and performa plurality of imaging events. For example, the bioassay system maydirect reaction solutions to flow along the reaction sites. At least oneof the reaction solutions may include four types of nucleotides havingthe same or different fluorescent labels. The nucleotides may bind tothe reaction sites, such as to corresponding oligonucleotides at thereaction sites. The bioassay system may then illuminate the reactionsites using an excitation light source (e.g., solid-state light sources,such as light-emitting diodes (LEDs)). The excitation light may have apredetermined wavelength or wavelengths, including a range ofwavelengths. The fluorescent labels excited by the incident excitationlight may provide emission signals (e.g., light of a wavelength orwavelengths that differ from the excitation light and, potentially, eachother) that may be detected by the light sensors.

As used herein, the term “immobilized,” when used with respect to abiomolecule or biological or chemical substance, includes substantiallyattaching the biomolecule or biological or chemical substance at amolecular level to a surface, such as to a detection surface of a lightdetection device or reaction structure. For example, a biomolecule orbiological or chemical substance may be immobilized to a surface of thereaction structure using adsorption techniques including non-covalentinteractions (e.g., electrostatic forces, van der Waals, and dehydrationof hydrophobic interfaces) and covalent binding techniques wherefunctional groups or linkers facilitate attaching the biomolecules tothe surface. Immobilizing biomolecules or biological or chemicalsubstances to the surface may be based upon the properties of thesurface, the liquid medium carrying the biomolecule or biological orchemical substance, and the properties of the biomolecules or biologicalor chemical substances themselves. In some cases, the surface may befunctionalized (e.g., chemically or physically modified) to facilitateimmobilizing the biomolecules (or biological or chemical substances) tothe surface.

In some examples, nucleic acids can be immobilized to the reactionstructure, such as to surfaces of reaction recesses thereof. Inparticular examples, the devices, biosensors, bioassay systems andmethods described herein may include the use of natural nucleotides andalso enzymes that are configured to interact with the naturalnucleotides. Natural nucleotides include, for example, ribonucleotidesor deoxyribonucleotides. Natural nucleotides can be in the mono-, di-,or tri-phosphate form and can have a base selected from adenine (A),Thymine (T), uracil (U), guanine (G) or cytosine (C). It will beunderstood, however, that non-natural nucleotides, modified nucleotidesor analogs of the aforementioned nucleotides can be used.

As noted above, a biomolecule or biological or chemical substance may beimmobilized at a reaction site in a reaction recess of a reactionstructure. Such a biomolecule or biological substance may be physicallyheld or immobilized within the reaction recesses through an interferencefit, adhesion, covalent bond, or entrapment. Examples of items or solidsthat may be disposed within the reaction recesses include polymer beads,pellets, agarose gel, powders, quantum dots, or other solids that may becompressed and/or held within the reaction chamber. In certainimplementations, the reaction recesses may be coated or filled with ahydrogel layer capable of covalently binding DNA oligonucleotides. Inparticular examples, a nucleic acid superstructure, such as a DNA ball,can be disposed in or at a reaction recess, for example, by attachmentto an interior surface of the reaction recess or by residence in aliquid within the reaction recess. A DNA ball or other nucleic acidsuperstructure can be performed and then disposed in or at a reactionrecess. Alternatively, a DNA ball can be synthesized in situ at areaction recess. A substance that is immobilized in a reaction recesscan be in a solid, liquid, or gaseous state.

FIGS. 1-8 illustrate a cross-section of a portion of a biosensor 100formed in accordance with one example. As shown, the biosensor 100 mayinclude a flow cell 102 that is coupled directly or indirectly to alight detection device 104. The flow cell 102 may be mounted to thelight detection device 104. In the illustrated example, the flow cell102 is affixed directly to the light detection device 104 through one ormore securing mechanisms (e.g., adhesive, bond, fasteners, and thelike). In some examples, the flow cell 102 may be removably coupled tothe light detection device 104.

The biosensor 100 and/or detection device 104 may be configured forbiological or chemical analysis to obtain any information or data thatrelates thereto. In particular examples, the biosensor 100 and/ordetection device 104 may comprise a nucleic acid sequencing system (orsequencer) configured for various applications, including but notlimited to de novo sequencing, resequencing of whole genomes or targetgenomic regions, and metagenomics. The sequencing system may beconfigured to perform DNA or RNA analysis. In some examples, thebiosensor 100 and/or detection device 104 is configured to perform alarge number of parallel reactions within the biosensor 100 and/ordetection device 104 to obtain information relating thereto.

The flow cell 102 may include one or more flow channels that direct asolution to or toward reaction sites 114 on the detection device 104, asexplained further below. The flow cell 102 and/or biosensor 100 maythereby include, or be in fluid communication with, a fluid/solutionstorage system (not shown) that may store various reaction components orreactants that are used to conduct the designated reactions therein, forexample. The fluid storage system may also store fluids or solutions forwashing or cleaning a fluid network and the biosensor 100 and/ordetection device 104, and potentially for diluting the reactants. Forexample, the fluid storage system may include various reservoirs tostore samples, reagents, enzymes, other biomolecules, buffer solutions,aqueous, oil and other non-polar solutions, and the like. As notedabove, the fluid or solution provided on the reaction structure 126 maybe relatively acidic (e.g., pH less than or equal to about 5) orbasic/alkaline (e.g., pH greater than or equal to about 8). Furthermore,the fluid storage system may also include waste reservoirs for receivingwaste products from the biosensor 100 and/or detection device 104.

In the illustrated example, the light detection device 104 includes adevice base 125 and a reaction structure 126 overlying the device base125, as shown in FIGS. 1 and 3-8 . In particular examples, the devicebase 125 includes a plurality of stacked layers (e.g., silicon layer orwafer, dielectric layer, metal-dielectric layers, etc.). The device base125 may include a sensor array 124 of light sensors 140, and a guidearray of light guides 118, as shown in FIG. 3 . As shown in FIGS. 1 and3-8 , the reaction structure 126 may include an array of reactionrecesses 108 that have at least one corresponding reaction site 114provided therein (e.g., immobilized on a surface thereof). In certainexamples, the light detection device 104 is configured such that eachlight sensor 140 corresponds (and potentially aligns) with a singlelight guide 118 and/or a single reaction recess 108 such that itreceives photons only therefrom. However, in other examples, a singlelight sensor 140 may receive photons through more than one light guide118 and/or from more than one reaction recess 108. A single light sensor140 may thereby form one pixel or more than one pixel.

As shown in FIG. 2 , the array of reaction recesses 108 and/or lightguides 118 (and potentially light sensors 140) may be provided in adefined repeating pattern such that at least some of the recesses 108and/or light guides 118 (and potentially light sensors 140) are equallyspaced from one another in a defined positional pattern. In otherexamples, the reaction recesses 108 and/or light guides 118 (andpotentially light sensors 140) may be provided in a random pattern,and/or at least some of the reaction recesses 108 and/or light guides118 (and potentially light sensors 140) may be variably spaced from eachother.

As shown in FIGS. 1 and 2 , the reaction structure 126 of the detectiondevice 104 may define a detector surface 112 over which a reactionsolution may flow and reside, as explained further below. The detectorsurface 112 of the reaction structure 126 may be the top exposed surfaceof the detection device 104. The detector surface 112 may comprise thesurfaces of the recesses 108 and interstitial areas 113 extendingbetween and about the recesses 108. As explained further below, thedevice base 125 of the detection device 104 may include a protectionlayer 130 that forms a smooth flat (e.g., planar) surface thatunderlying the support structure that minimizes surface topographymodulation induced in the detector surface 112, and in particular to theinterstitial areas 113 of the detector surface 112. In particularexamples, the interstitial areas 113 of the detector surface 112 may besmooth planar surface portions that prevent the reaction solution and/orany other biological or chemical substances from remaining thereonand/or prevents pad hopping errors. The smoothness and/or flatness ofthe interstitial areas 113 of the detector surface 112 provided by theconfiguration of the underlying protection layer 130 may be smootherand/or flatter than as compared to examples that are void of theprotection layer 130. Further, in some examples, the smoothness and/orflatness of the interstitial areas 113 of the detector surface 112provided by the underlying protection layer 130 may enhance therobustness of the detection device 104 as compared to examples that arevoid of the protection layer 130.

The detector surface 112 of the light detection device 104 may befunctionalized (e.g., chemically or physically modified in a suitablemanner for conducting designated reactions). For example, the detectorsurface 112 may be functionalized and may include a plurality ofreaction sites 114 having one or more biomolecules immobilized thereto,as shown in FIGS. 1, 3 and 4 . As noted above, the detector surface 112may include an array of reaction recesses 108 (e.g., open-sided reactionchambers). Each of the reaction recesses 108 may include one or more ofthe reaction site 114. The reaction recesses 108 may be defined by, forexample, a change in depth (or thickness) along the detector surface112. In other examples, the detector surface 112 may be substantiallyplanar.

As shown in FIGS. 3 and 4 , the reaction sites 114 may be distributed ina pattern along the detector surface 112, such as within the reactionrecesses 108. For instance, the reactions sites 114 may be located inrows and columns along the reaction recesses 108 in a manner that issimilar to a microarray. However, it is understood that various patternsof reaction sites 114 may be used. The reaction sites 114 may includebiological or chemical substances that emit light signals, as explainedfurther below. For example, the biological or chemical substances of thereactions sites 114 may generate light emissions in response to theexcitation light 101. In particular examples, the reaction sites 114include clusters or colonies of biomolecules (e.g., oligonucleotides)that are immobilized on the detector surface 112 within the reactionrecesses 108. The reactions sites 114 may generate light emissions inresponse to incident excitation light after treatment with the reactionsolution. For example, the reaction solution may initiate a reactionand/or form a reaction product at the reactions sites 114 (butpotentially not at other reaction sites of the reaction structure 126 ofthe device 104) that generates light emissions in response to theexcitation light.

As shown in FIG. 1 , in one example the flow cell 102 includes at leastone sidewall and a flow cover 110. The at least one sidewall may becoupled to the detector surface 112 and extend between the flow cover110 and the detector surface 112. The flow cell 102 may be configured sothat a flow channel 119 is formed between the flow cover 110 and thedetector surface 112 of the light detection device 104. In someexamples, the flow channel 119 may include a height (extending betweenthe flow cover 110 and the detector surface 112) within the range ofabout 50 to about 400 μm (microns), or more particularly about 80 toabout 200 μm, for example. In one example, the height of the flowchannel 119 is about 100 μm. The flow cover 110 may comprise a materialthat is transparent to the excitation light 101 propagating from anexterior of the biosensor 100 and toward/into the flow channel 119, asshown in FIG. 1 . It is noted that excitation light 101 may approach theflow cover 110 from any angle, and along the same or different angles.

The excitation light 101 may be emitted from any illumination source(not shown), which may or may not be part of the bioassay system,biosensor 100 or light detection device 104. In some examples, theillumination system may include a light source (e.g., one or more LED)and, potentially, a plurality of optical components to illuminate atleast the reaction structure 126 of the detection device 104. Examplesof light sources may include lasers, arc lamps, LEDs, or laser diodes.The optical components may be, for example, reflectors, dichroics, beamsplitters, collimators, lenses, filters, wedges, prisms, minors,detectors, and the like. In a particular example, the illuminationsystem is configured to direct the excitation light 101 to reactionsites 114 within the recesses 108 of the reaction structure 126 of thedetection device 104. In some examples, the illumination system may emitthe excitation light 101 within a range of wavelengths, such as withinthe range of about 300 nm to about 700 nm for example, or moreparticularly within the range of about 400 nm to about 600 nm forexample. In some examples, the illumination system may emit theexcitation light 101 at a certain wavelength or wavelengths that excitesthe biological or chemical substance(s) of the reaction sites 108 (e.g.,a reaction initiated by the reaction solution and/or reaction productform by the reaction solution at the reactions sites 114) to emit lightemissions of a differing wavelength or wavelengths. For example, in oneexample where the reaction sites 108 include fluorophores excited bygreen wavelengths of light, the excitation light may be about 532 nm andthe light emissions may be about 570 nm or more.

As also shown in FIG. 1 , the flow cover 110 may include at least oneport 120 that is configured to fluidically engage the flow channel 119and, potentially, other ports (not shown). For example, the other portsmay be from a cartridge or a workstation that comprised the reactionsolution or another biological or chemical substance. The flow channel119 may be configured (e.g., sized and shaped) to direct a fluid orsolution, such as the reaction solution, along the detector surface 112.

FIGS. 3 and 4 show the detection device 104 in greater detail than FIG.1 . More specifically, FIGS. 3 and 4 show a single light sensor 140, asingle light guide 118 for directing and passing light emissions from atleast one reaction site 114 associated therewith toward the light sensor140, and associated circuitry 146 for transmitting signals based on thelight emissions (e.g., photons) detected by the light sensor 140. It isunderstood that the other light sensors 140 of the sensor array 124(FIGS. 1 and 2 ) and associated components may be configured in anidentical or similar manner. It is also understood, however, the lightdetection device 104 is not required to be manufactured uniformlythroughout. Instead, one or more light sensors 140 and/or associatedcomponents may be manufactured differently or have differentrelationships with respect to one another.

The circuitry 146 may include interconnected conductive elements (e.g.,conductors, traces, vias, interconnects, etc.) that are capable ofconducting electrical current, such as the transmission of data signalsthat are based on detected photons. For example, in some examples, thecircuitry 146 may comprise a microcircuit arrangement. The lightdetection device 104 and/or the device base 125 may comprise at leastone integrated circuit having an array of the light sensors 140. Thecircuitry 146 positioned within the detection device 104 may beconfigured for at least one of signal amplification, digitization,storage, and processing. The circuitry 146 may collect (and potentiallyanalyze) the detected light emissions and generate data signals forcommunicating detection data to a bioassay system. The circuitry 146 mayalso perform additional analog and/or digital signal processing in thelight detection device 104.

The device base 125 and the circuitry 146 may be manufactured usingintegrated circuit manufacturing processes, such as processes used tomanufacture charged-coupled devices or circuits (CCD) orcomplementary-metal-oxide semiconductor (CMOS) devices or circuits. Forexample, as shown in FIG. 3 , the device base 125 may be a CMOS devicecomprising of a plurality of stacked layers including a sensor base 141,which may be a silicon layer (e.g., a wafer) in some examples. Thesensor base 141 may include the light sensor 140, and gates 143 formedthereon. The gates 143 may be electrically coupled to the light sensor140. When the light detection device 104 is configured as shown in FIG.3 , the light sensor 140 may be electrically coupled to the circuitry146 through the gates 143, for example.

At least some of the circuitry 146 may be provided within devicesubstrate layers of the device base 125 of the detection device 104,through/into which the lights guides 118 may each extend. In someexamples, each of the substrate layers may include interconnectedconductive elements that forms at least part of the device circuitry146, and dielectric material 142 adjacent to (and potentiallysurrounding) the conductive elements of the circuitry 146, as shown inFIG. 3 . The conductive elements of the circuitry 146 may be embeddedwithin the dielectric material 142. As also shown in FIG. 3 , the lightsguides 118 may extend through the dielectric material 142 and may bespaced from the circuitry 146. Various metallic elements and/ordielectric materials may be used, such as those suitable for integratedcircuit manufacturing (CMOS manufacturing). For example, in someexamples, the conductive elements/circuitry 146 may be metallicelements, such as W (tungsten) elements, Cu (copper) elements, Al(aluminum) elements, or a combination thereof (but it is understood thatother materials and configurations may be used). In some examples, thedielectric material may be SiO2 (but it is understood that othermaterials and configurations may be used).

As used herein, the term “layer” is not limited to a single continuousbody of material unless otherwise noted. For example, the sensor base141 and/or the device layers of the device base 125 may include multiplesub-layers that are different materials and/or may include coatings,adhesives, and the like. Furthermore, one or more of the layers (orsub-layers) may be modified (e.g., etched, deposited with material,etc.) to provide the features described herein.

As shown in FIGS. 3 and 4 , the reaction structure 126 may comprise oneor more layers that form the reaction recesses 104 extending therein.The reaction structure 126 may extend along a top outer surface of thedevice base 125. In the illustrated example, the reaction structure 126is deposited directly along the top outer surface of a first shieldlayer 154 and the first and second filter material 116, 115 of thedevice base 125, as described further below. However, an interveninglayer may be disposed between the reaction structure 126 and the devicebase 125 in other examples. The reaction structure 126 may include oneor more materials that are configured to allow the excitation lightsignals 101 and emitted light signals from the reaction sites 114 (aftertreatment with the reaction solution) within the recesses 108 to passtherethrough and into an opening 158 of one or more light guide 118corresponding to a particular reaction recess 108. In some examples, thereaction structure 126 may include one more layer or other feature thatprevents crosstalk or “sharing” of emitted light from a particularreaction site 114/reaction recess 108 from passing to anon-corresponding sensor 140.

The reaction structure 126 may comprise a plurality of differing layers,as shown in FIGS. 3 and 4 . In the illustrated example, the reactionstructure 126 may include a first reaction layer 160 that extends over(directly or indirectly) device base 125 (e.g., over the first shieldlayer 154) and the opening 158 of the light guides 118 (e.g., the firstand second filter material 116, 115) of the device base 125, as shown inFIGS. 3 and 4 . As also shown in FIGS. 3 and 4 , in the illustratedexample, the reaction structure 126 further includes a second layer 162that extends over (directly or indirectly) the first layer 160. Thereaction structure 126 of illustrated example also includes a thirdlayer 164 that extends over (directly or indirectly) the second layer162, and a fourth layer 166 that extends over (directly or indirectly)the third layer 164. The reaction recesses 108 may extend at least intothe third layer 164.

The fourth layer 166 may form the inner surfaces (e.g., side walls and abottom wall) of the reaction recesses 108 by extending over anindentation (e.g., a cavity or a void) in the third layer 164, as shownin FIGS. 3 and 4 . The fourth layer 166, and potentially the secondlayer 162, may form the detector surface 112, as shown in FIGS. 3 and 4. In some cases, the fourth layer 166, and potentially the second layer162, may be configured to provide a solid surface that permitschemicals, biomolecules or other analytes-of-interest to be immobilizedthereon. For example, each of the reaction sites 114 may include acluster of biomolecules that are immobilized to the detector surface112, which may comprise the fourth layer 166, and potentially the secondlayer 162. Thus, the fourth layer 166, and potentially the second layer162, may comprise a material that permits the reaction sites 114 to beimmobilized thereto. The first layer 160 and the fourth layer 166 (andpotentially the second layer 162 and the third layer 166) may comprise amaterial that is at least substantially transparent to the excitationlight 101 and the emission light of the reaction sites 114. In addition,the fourth layer 166, and potentially the second layer 162, may bephysically or chemically modified to facilitate immobilizing thebiomolecules and/or to facilitate detection of the light emissions.

By way of example and as shown in the illustrated example of FIGS. 3 and4 , the first layer 160 and the third layer 166 may comprise a firstmaterial, and the second layer 162 and the fourth layer 166 may comprisea second material that differs from the first material. In some suchexamples, the first material is SiN, and the second material is TaO.However, the reaction structure 126 may comprise differing layers (e.g.,different layers, fewer layers, and/or additional layers) and/ordiffering materials.

As shown in FIGS. 3 and 4 , the device base 125 of the detection device104 may include a first shield layer 150 that extends over (directly orindirectly) the stacked layers (e.g., metal-dielectric layers) of thedevice base 125, such as over the dielectric material 142 and theconductive circuitry components 146. The first shield layer 150 mayinclude a material that is configured to block, reflect, and/orsignificantly attenuate the excitation light 101 and/or the lightemissions from the reaction sites 114 (e.g., light signals that arepropagating from the flow channel 118). By way of example only, thefirst shield layer 150 may comprise tungsten (W).

The first shield layer 150 may include at least one an aperturetherethrough which aligns, at least partially, with at least onecorresponding light guide 118. The first shield layer 150 may include anarray of such apertures. In some examples, the first shield layer 150may extend entirely about the apertures therein. As such, the lightsignals from excitation light 101 and/or the light emissions from thereaction sites 114 may be blocked, reflected, and/or significantlyattenuated to prevent the light signals from passing through the devicebase 125 outside of the light guides 118 and being detected by the lightsensors 140. In some examples, the first shield layer 150 extendscontinuously between adjacent light guides 118 and/or openings extendingthereto. In some other examples, the first shield layer 150 does notextend continuously between adjacent light guides 118 and/or openingsextending thereto such that one or more other opening exists in thefirst shield layer 150, which may allow the excitation light 101 and/orthe light emissions from the reaction sites 114 to pass therethrough.

In some examples, the device base 125 of the detection device 104 mayinclude a second shield layer 152 that extends over (directly orindirectly) the first shield layer 150, as shown in FIGS. 3 and 4 . Thesecond shield layer 152 may include anti-reflective material and/or amaterial that prevents contamination of the underlying portions of thedevice base 125. By way of example only, the second shield layer 152 maycomprise SiON. In some examples, the second shield layer 152 may beconfigured to prevent contaminated, such as sodium, from interactingwith the first shield layer 150, the dielectric material 142 and/or theconductive (e.g., metal) components of the device circuitry 146. In someexamples, the second shield layer 152 may mimic the configuration of thefirst shield layer 150. For example, the second shield layer 152 mayinclude at least one aperture therethrough which aligns, at leastpartially, with at least one light guide 118, as shown in FIGS. 3 and 4. The second shield layer 152 may include an array of such apertures. Insome examples, the second shield layer 152 may extend about theapertures therein. In some examples, the second shield layer 152 extendscontinuously between adjacent light guides 118 and/or openings extendingthereto. In some other examples, the second shield layer 152 does notextend continuously between adjacent light guides 118 and/or openingsextending thereto such that one or more other aperture exists in thesecond shield layer 152, as shown in FIGS. 3 and 4 .

In some examples, the light detection device 104 may include a linerlayer 154 that extends over the device base 125 and about the lightguides 118, as shown in FIGS. 3 and 4 . The liner layer 154 may be acontinuous conformal layer formed on the device base 125. The linerlayer 154 may be chemically reactive with respect to the reactionsolution. For example, due to the composition (e.g., water and/or oil)and/or relatively high acidity (e.g., pH equal to or less than about 5)or relatively high basicity (e.g., pH equal to or greater than about 8)of the reaction solution, the reaction solution may chemically reactwith the material of the liner layer 154 when exposed thereto and causethe material to be dissolved or otherwise detached (i.e., etch the linerlayer 154). Over exposure time, the reaction solution may thereby etchthrough the liner layer 154 and, ultimately, interact with and corrodeor otherwise interfere with the functioning of the device circuitry 146.For example, the liner layer 154 may be a silicon nitride layer (orotherwise include SiN), and the relatively high acidic or basic reactionsolution may tend to etch the SiN when exposed thereto. In this way, theSiN liner layer 154 may be ineffective in preventing the reactionsolution from etching therethrough and, ultimately, interacting with thedevice circuitry 146 (e.g., corroding the conductive (e.g., metal)components of the device circuitry 146). Other materials forming theliner layer 154 may be similarly chemically reactive to the reactionsolution, such as due to the composition and/or relatively high acidityor basicity thereof, and thereby fail to prevent the reaction solutionfrom etching therethrough over time.

The liner layer 154 may be void of defined apertures. However, the linerlayer 154 may include at least one internal discontinuity, pore, crack,break or the like that allows a liquid or solution, such as the reactionsolution, to flow through the liner layer 154, as explained furtherbelow. For example, the density of the liner layer 154 may be relativelylow such that internal discontinuities thereof form a pathway throughthe liner layer 154, through which the reaction solution may pass to thedielectric material 142 and, ultimately, the conductive (e.g., metal)components of the device circuitry 146. In this way, the liner layer 154may be ineffective in preventing the reaction solution from passingtherethrough and, ultimately, interacting with the device circuitry. Insome example, due to its density or internal discontinuities, the linerlayer 154 may not be liquid impervious.

In the illustrated examples, the liner layer 154 extends between thesecond shield layer 152 and the protection layer 130 on the top upperportion of the device base 125, and extends along the light guides 118between the dielectric material layers 142 and the protection layer 130.The liner layer 154 may be configured as an anti-reflective or areflective layer (e.g., to ensure the light emitted from the reactionsites 114 passes through the light guides 118), a contaminationprevention layer (e.g., to prevent sodium contamination into the devicebase 125) and/or an adhesion layer (e.g., to adhere the filter material116 of the light guides 118 to the dielectric material 142). In someexamples, the liner layer 154 may be configured as a contaminationprevention layer that prevents any ionic species from penetrating intodevice layers (e.g., metal-dielectric layers). In some examples, theliner layer 154 comprises SiN. In some examples, the liner layer 154comprises a SiN layer.

As shown in FIGS. 3 and 4 , the liner layer 154 may be of asubstantially uniform thickness. In other examples, the thickness of theliner layer 154 may vary. For example, the portions of the liner layer154 extending over the top portion of the device base 125 may be a firstthickness, and the portions of the liner layer 154 extending about thelight guides 118 may be a second thickness that is thicker or thinnerthan the first thickness. As another example, the thickness of theportions of the liner layer 154 extending about the light guides 118 mayvary along the depth within the device base 125 (e.g., may taper withdepth into the device base 125). In some examples, the thickness of theliner layer 154 may be within the range of about 10 nm to about 100 nm.In the illustrated example, the liner layer 154 is about 50 nm thick.

As shown in FIG. 3 , the device base 125 may also include a second linerlayer 155 formed within the device layers of the device base 125 andbeneath the light guides 118. The second liner layer 155 may besubstantially similar or the same as the liner layer 154 but for itsposition within the device base 125. In some examples, the second linerlayer 155 may extend immediately below the protection layer 130 alongthe bottom of the light guides 118, as shown in FIG. 3 . In this way,the liner layer 154 and the second liner layer 155 may extend entirelyabout the light guides 118 but for the openings 158 of the light guides118 beneath the recesses 108. The second liner layer 155 may form thebottom of the light guides 118.

As discussed above, the device base 125 of the detection device 104 mayinclude the protection liner layer 130 positioned between each lightguide 118 and the device circuitry 146, as shown in FIGS. 3 and 4 . Theprotection layer 130 may extend over (directly or indirectly) the linerlayer 154 on top of the device base 125 and along the light guides 118,as shown in FIGS. 3 and 4 . In some other examples (not shown), theprotection layer 130 may not extend over (directly or indirectly) thetop of the device base 125 beneath the reaction structure 126, and mayonly extend along/about the light guides 118 within the device base 126(i.e., only be positioned between the dielectric material 142 and thefilter material 116).

The protection layer 130 may extend fully about the filter material 116of the light guides 118 but for the openings 158 thereof. For example,the protection layer 130 may extend about the side surfaces of the lightguides 118, and below the light guides 118 (between the liner layer 154and the second liner layer 155 and the filter material 116). Theprotection layer 130 may also be provided on the device base 125 (e.g.,directly over the liner layer 154) and the reaction structure 126. Theprotection layer 130 may also thereby be provided over the top portionof device base 125 and positioned between the device base 125 and thereaction structure 126.

The protection layer 130 may be a continuous coating layer. Theprotection layer 130 may be void of predefined or purposely-formedapertures or other voids that would allow a liquid or solution, such asthe reaction solution, to flow therethrough. The protection layer 130may also be void of any internal discontinuities, pores, cracks, breaksor the like, or prevent the formation thereof, that would allow a liquidor solution, such as the reaction solution, to flow therethrough, asexplained further below. The protection layer 130 may thereby be aliquid impervious barrier. A liquid impervious layer herein refers to alayer that may prevent any liquid or solution (e.g., the reactionsolution) from passing therethrough, such as preventing at least about99 vol % of the reaction solution in contact with the protection layer130 at about atmospheric pressure from passing therethrough. Theprotection layer 130 may also be chemically inert with respect to thereaction solution such that the reaction solution (which may include arelatively high acidity or relatively high basicity, as described above)does not etch the protection layer 130, or etches less than about one(1) angstrom (A) of the thickness of the protection layer 130 per hourat about 100 degrees Celsius and at about atmospheric pressure, when thereaction solution is in contact with the protection layer 130. Forexample, the composition of the protection layer 130 may not chemicallyreact, or chemically reacts to only a relatively small degree, with thecomposition of the reaction solution (which may include a relativelyhigh acidity or relatively high basicity) such that the reactionsolution does not etch the protection layer 130 or etches less thanabout one (1) angstrom (A) of the thickness of the protection layer 130per hour at about 100 degrees Celsius and at about atmospheric pressurewhen the reaction solution is in contact with the protection layer 130.The liner layer 154 may thereby comprise an etch resistant layer withrespect to the reaction solution (which may include a pH equal to orless than about 5 or a pH equal to or greater than about 8, for example)to prevent the reaction solution from penetrating therethrough (overtime) and, ultimately, interacting with and corroding or otherwiseinterfering with the functioning of the device circuitry 146. Theprotection layer 130 is thereby configured to prevent a liquid orsolution (such as the reaction solution) that may penetrate through thereaction structure 126 to the protection layer 130, or through thereaction structure 126 and the filter material 116 of a light guide 118to the protection layer 130, from interacting with the device circuitry146 (and the liner layer 154 (if provided) and the dielectric material142).

The thickness of the protection layer 130 may vary. For example, theportions of the protection layer 130 extending over the top portion ofthe device base 125 may be a first thickness, and the portions of theprotection layer 130 extending about the light guides 118 and/or belowthe light guides 118 may be a second thickness that is thicker orthinner than the first thickness. As another example, the thickness ofthe portions of the protection layer 130 extending about the lightguides 118 may be vary along the depth of the light guides 118 withinthe device base 125. In such an example, the thicknesses of the portionsof the protection layer 130 extending about the light guides 118 maytaper (i.e., narrow or thin) as it extends into the device base 125 fromthe opening 158 of the light guides 118. The protection layer 130 may bea conformal coating layer. In the illustrated example shown in FIG. 3 ,the protection layer 130 is of a substantially uniform thickness. Insome examples, the thickness of the liner layer 154 may be within therange of about 10 nm to about 1 micron, within the range of about 5 nmto about 100 nm, or within the range of about 50 nm to about 100 nm. Inthe illustrated example, the liner layer 154 is about 50 nm thick.

The protection layer 130 may comprise any material such that it preventsany solution or liquid, such as the reaction solution, that maypenetrate through the reaction structure 126, or the reaction structure126 and a light guide 118, from interacting with the device circuitry146, and allows the light emitted from the reaction sites 114 (aftertreatment with the reaction solution) to pass therethrough and to atleast one corresponding light sensor 140 (via at least one correspondinglight guide 118). For example, the protection layer 130 may comprise anymaterial that allows light emitted from the reaction sites 114 that isnot filtered by the filter material 116 to pass therethrough, and thatis chemically inert to the reaction solution. For example, theprotection layer 130 may comprise any material that does not chemicallyreact, or chemically reacts to only a relatively small degree, with thereaction solution (which may include a pH equal to or less than about 5or a pH equal to or greater than about 8, for example) such that thereaction solution does not etch the protection layer 130 or etches lessthan about one (1) angstrom (A) of the thickness of the protection layer130 per hour at about 100 degrees Celsius and at about atmosphericpressure when the reaction solution is in contact with the protectionlayer 130. For example, the protection layer 130 may comprise at leastone oxide, at least one nitride, or a combination thereof. In someexamples, the protection layer 130 may comprise silicon dioxide, a metaloxide, a metal nitride or a combination thereof. In some examples, theprotection layer 130 may comprise silicon dioxide, silicon oxynitride,silicon monoxide, silicon carbide, silicon oxycarbide, siliconnitrocarbide, silicon dioxide, metal oxide, metal nitride or acombination thereof. In some examples, the pH of the reaction solutionis greater than or equal to about 8, and the protection layer 130comprises silicon dioxide, silicon oxynitride, silicon monoxide, siliconcarbide, silicon oxycarbide, silicon nitrocarbide, silicon dioxide,metal oxide, metal nitride or a combination thereof. In some examples,the pH of the reaction solution is less than or equal to about 5, andthe protection layer 130 comprises silicon carbide, silicon oxycarbide,silicon nitrocarbide, a metal oxide, a metal nitride or a combinationthereof. It is noted that the thickness, formation process and materialof the protection layer 130 may be considered and configured(independently or collectively) such that the protection layer 130prevents any solution or liquid, such as the reaction solution, that maypenetrate through the reaction structure 126, or the reaction structure126 and a light guide 118, from ultimately interacting with the devicecircuitry 146 (and the liner layer 154 (if provided) and the dielectricmaterial 142).

As discussed above, the light guides 118 may extend from an opening 158into the device base 125, such as through the dielectric material layers142 and toward at least one light detection sensor 140. In particularexamples, the light guides 118 are elongated and extend from proximateto at least one corresponding reaction recess 108 (from the aperture 158thereof) toward at least one corresponding light sensor 140 within thesensor base 141. The light guides 118 may extend lengthwise along acentral longitudinal axis. The light guides 118 may be configured in athree-dimensional shape that allows and/or promotes the light emittedfrom the reaction site(s) 114 of at least one corresponding reactionrecess 108 to at least one corresponding light sensor 140, such assubstantially cylindrical or frustro-conical shape with a circularopening 158. The longitudinal axis of the light guides 118 may extendthrough a geometric center of the cross-section. However, othergeometries may be used in alternative examples. For example, thecross-section of the light guides 118 may be substantially square-shapedor octagonal.

The light guides 118 may comprise a filter material 116 configured tofilter the excitation light 101 or a range of wavelengths including thatof the excitation light 101, and permit the light emissions from atleast one reaction site 114 of at least one corresponding reactionrecess 108 (or a range of wavelengths including that of the lightemissions) to propagate therethrough and toward at least onecorresponding light sensor 140. The light guides 118 may be, forexample, an absorption filter (e.g., an organic absorption filter) suchthat the filter material 116 absorbs a certain wavelength (or range ofwavelengths) and allows at least one predetermined wavelength (or rangeof wavelengths) to pass therethrough. By way of one example only, theexcitation light may be about 532 nm and the light emissions from the atleast one reaction site 114 may be about 570 nm or more, and thereforethe filter material 116 may absorb light of wavelengths of about 532 nmor less than about 570 nm, and allow light of wavelengths of about 570nm or more to pass therethrough. Each of the light guides 118 of thearray may include substantially the same filter material 116, ordiffering light guides 118 may include differing filter material 116.

Each light guide 118 may thereby be configured relative to surroundingmaterial of the device base 125 (e.g., the dielectric material 142) toform a light-guiding structure. For example, the light guides 118 mayhave a refractive index of at least about 2. In certain examples, thelight guide 118 is configured such that the optical density (OD) orabsorbance of the excitation light is at least about 4 OD. Morespecifically, the filter material 116 of the light guides 118 may beselected and the light guide 118 may be dimensioned to achieve at leastabout 4 OD. In more particular examples, the light guide 118 may beconfigured to achieve at least about 5 OD, or at least about 6 OD.

Initially, the reaction sites 114 of one or more reaction recesses 108of the reaction structure 126 of the device 104 or biosensor 100 may notinclude a designated reaction, which is generally represented by thelack of shading/patterning in FIG. 4 . As discussed above, a reactionsite 114 may include biological or chemical substances immobilized tothe detector surface 112 or, more specifically, on the base and/or sidesurfaces of the reaction recesses 108. In particular examples, thereaction sites 114 are located proximate to an opening 158 of at leastone corresponding light guide 118 so that pre-designated light emissionsemitted from the reaction sites 114 after a designated reaction hasoccurred via treatment with the reaction solution propagate through thereaction structure 126, through the opening 158 and the filter material116 of at least one corresponding light guide 118, through theprotection liner layer (and potentially the first and second shieldlayers 154, 155), and to at least one corresponding light sensor 140.

The biological or chemical substances of a single reaction site 114 maybe similar or identical (e.g., a colony of analytes (e.g.,oligonucleotides) that have a common sequence). However, in otherexamples, a single reaction site 114 and/or reaction recess may includediffering biological or chemical substances. Before a designatedreaction, the reaction sites 114 may include at least one analyte (e.g.,an analyte-of-interest). For example, the analyte may be anoligonucleotide or a colony thereof (e.g., anoligonucleotide-of-interest). The oligonucleotides may have aneffectively common sequence and bind with a predefined or particularfluorescently labeled biomolecule, such as a fluorescently-labelednucleotide.

However, prior to the designated reaction, the fluorophores of thefluorescently labeled biomolecule are not incorporated or bonded to thebiological or chemical substances (e.g., an oligonucleotides) at thereaction sites 114, as shown in FIG. 4 . To achieve the designatedreaction (i.e., to incorporate a fluorescently labeled biomolecule withthe biological or chemical substances of the reaction sites 114), theflow cell may provide a flow of the reaction solution 170 to thereaction structure 126, as shown in FIG. 5 . The reaction solution maycomprise one or more sequencing reagents utilized for DNA grafting,clustering, cleaving, incorporating and/or reading, for example.However, the reaction solution 170 may be any solution. In someexamples, the reaction solution 170 may include a liquid. For example,the reaction solution 170 may be an aqueous solution and/or may becomprised of an oil; however, it is understood that the reactionsolution 170 may comprise any other liquid. The reaction solution 170may include one or more constituents that would tend to react with,corrode, dissolve, deteriorate or otherwise render the circuitry 146inoperable or less effective as circuitry (i.e., transferring signals orelectrons). For example, the reaction solution 170 may be an aqueoussolution that would tend to oxidize the metal portions of the circuitry146 if it interacted therewith.

In one example, the reaction solution 170 contains one or morenucleotide types, at least some of which are fluorescently-labeled, andthe reaction solution 170 also contains one or more biomolecules, suchas polymerase enzymes, which incorporate nucleotides into a growingoligonucleotide at the reaction site 114, thereby labeling theoligonucleotide with a fluorescently-labeled nucleotide. In thisimplementation, a flow cell may provide a wash solution to remove anyfree nucleotides that did not incorporate into oligonucleotides. Thereaction sites 114 can then be illuminated with an excitation light 101of at least a first wavelength, causing fluorescence of a second and/orthird wavelength in those reaction sites 114 where afluorescently-labeled nucleotide was incorporated. Reaction sites 114that did not incorporate a fluorescently-labeled nucleotide do not emitlight upon incident excitation light 101.

As shown in the illustrated example in FIG. 5 , the reaction solution170 may be provided within the reaction recesses 108 to achieve thedesignated reaction of the at least one fluorescently-labeled moleculebinding or incorporating with the biological or chemical substances ofthe reaction sites 114. In some examples, the biological or chemicalsubstances of the reaction sites 114 may be an analyte, and thefluorescently-labeled molecule may include at least one fluorophore thatbonds or incorporates with the analyte. In such examples, the analytemay comprise an oligonucleotide, and the at least onefluorescently-labeled molecule comprises a fluorescently-labelednucleotide.

When the biological or chemical substances (e.g., oligonucleotides) ofthe reaction sites 114 are similar or identical, such as having a commonsequence, the reaction sites 114 may be configured to generate commonlight emissions after the designated reactions and the excitation light101 is absorbed by the fluorescently-labeled molecules bonded orincorporated therewith from the reaction solution 170. When thebiological or chemical substances (e.g., oligonucleotides) of thereaction sites 114 are not similar or identical, such as having adiffering sequence, the reaction sites 114 may be configured to generatediffering light emissions after the designated reactions and theexcitation light 101 is absorbed by the fluorescently-labeled moleculesbonded or incorporated therewith from the reaction solution 170. Thefilter material 116 of the light guides 118 may be selected orconfigured to allow any of such light emissions to propagatetherethrough and to the light sensors 140, but prevent other such lightemissions and/or the excitation light to pass therethrough to the lightsensors 140.

As shown FIG. 6 , after the reaction solution 170 has interacted withthe biological or chemical substances (e.g., oligonucleotides) of thereaction sites 114, the designated reactions have occurred such that thereaction sites 114 include fluorescently-labeled molecules, such asfluorophores, that emit light of a predefined wavelength or range ofwavelengths when excited by the excitation light 101 (i.e., when theexcitation light 101 is incident upon the reaction sites 114). Theexcitation light 101 may thereby be configured based on thefluorescently-labeled molecules of the reaction solution 170 (orvice-versa) and/or a reaction initiated by the reaction solution 170 atthe reaction sites 114 and/or a reaction product formed by the reactionsolution 170 at the reaction sites 114. As shown in FIG. 6 , thereaction sites 114 may emit light signals 172 of a wavelength thatdiffers from excitation light 101 when excited by the excitation light101 after a designated reaction has occurred via treatment with thereaction solution.

The emitted light 172 from the reaction sites 114 (after treatment withthe reaction solution) may travel in all directions (e.g.,isotropically) such that, for example, a portion of the light 172 isdirected into the at least one corresponding light guide 118, and aportion of the light 172 is directed into the flow channel 119 or thereaction structure 126, as shown in FIG. 6 . For the portion that passesinto the light guide 118, the device 104 (e.g., the light guides 118thereof) is configured to facilitate detection of the photons by the atleast one corresponding light sensor 140. Specifically, the emittedlight 172 from the reaction sites 114 that passes through the opening ofa corresponding light guide 118 will be propagated through the filtermaterial 116 thereof to the light sensor 140. The excitation light 101,however, will be absorbed or otherwise prevented from propagatingthrough the light guide 118 to the light sensor 140 by the filtermaterial 116, as shown in FIG. 6 . The device circuitry 146 that iselectrically coupled to the light sensors 140 transmits data signalsbased on the photons detected by the light sensors 140. In this way,only the presence of a designated reaction at a reaction site 114 viatreatment with the reaction solution will cause emitted light 172 to bedetected by the light sensors 140 during a light detection event.

As shown in FIG. 6 , a portion of the emitted light 172 from thereaction sites(s) 114 that passes into the at least one correspondinglight guide 118 may propagate directly through the filter material 116thereof and to the at least one corresponding light sensor 140. Forexample, at least a majority of the emissive light 172 from the reactionsites(s) 114 that passes into the at least one corresponding light guide118 via the opening 158 may pass directly (e.g., linearly orsubstantially linearly) through the filter material 116 to the at leastone corresponding light sensor 140. A small amount of the emissive light172 from the reaction sites(s) 114 that passes into the at least onecorresponding light guide 118 may travel at an angle such that it passesthrough the protection layer 130, the liner layer 154 and into thedielectric material layers 142. Such light may be reflected by thecircuitry 146 or other metal or reflective structures embedded withinthe dielectric material layers 142, and potentially back into thecorresponding light guide 118 (and potentially to the at least onecorresponding light sensor 140). In some examples, the protection layer130 and/or the liner layer 154 may be transparent to light, such astransparent or substantially transparent at least to the emissive light172 from the reaction sites(s) 114.

FIGS. 7 and 8 illustrate an example of the device 104 that includescracks or other discontinuities 178 in the reaction structure 126 andthe filter material 116 of a light guide 118. As shown in FIGS. 7 and 8, the reaction structure 126, and potentially the filter material 116 ofat least one light guide 118, may include cracks or otherdiscontinuities 178 that extend from the detection surface 112 to theprotection layer 130. The discontinuities 178 may extend from thedetection surface 112 through the reaction structure 126 to theprotection layer 130, and/or extend from the detection surface 112through the reaction structure 126 and the filter material 116 to theprotection layer 130. The discontinuities 178 may thereby allow asolution or liquid to flow from the detection surface 112 into thedetection device 104 and interact with the protection layer 130.

It is noted that the discontinuities 178 or other pathways may not be asdefined and/or continuous as the depicted discontinuities 178. Rather,the discontinuities 178 represent any pathway that a liquid or solutionmay take through the reaction structure 126 (i.e., from the detectionsurface 112) to the protection layer 130. For example, any pathwayextending through the reaction structure 126 from the detection surface112 (e.g., extending through the first layer 160, second layer 162,third layer 164 and fourth layer 166 (if present)) to the protectionlayer 130 may ultimately allow a liquid or solution (e.g., the reactionsolution) to interact with the protection layer 130. As another example,any pathway extending through the reaction structure 126 from thedetection surface 112 (e.g., extending through the first layer 160,second layer 162, third layer 164 and fourth layer 166 (if present)) andat least one light guide 118 (e.g., extending through the opening 158and the filter material 116) to the protection layer 130 may ultimatelyallow a liquid or solution (e.g., the reaction solution) to interactwith the protection layer 130. The discontinuities 178 represent anysuch pathways.

The discontinuities 178 extending through the reaction structure 126,and/or extending the through the reaction structure 126 and at least onelight guide 118, may be formed by any process or mechanism. For example,the discontinuities 178 extending through the reaction structure 126,and/or extending the through the reaction structure 126 and at least onelight guide 118, may be formed during the manufacturing stage(s) of thedevice 104, and/or during use of the device 104, for example. As onespecific mode of formation, the discontinuities 178 may be caused bydiffering thermal expansion coefficients of the materials of the device104, which may cause the discontinuities 178 to form during themanufacturing stage(s) of the device 104 and/or during use of the device104. As another example, the discontinuities 178 may be formed by errorsin, or naturally occur from, the formation process of the reactionstructure 126 and/or the light guides 118. As yet another example, thediscontinuities 178 may be formed by the reaction solution or any otherliquid or solution) from reacting with and etching through the reactionstructure 126 and/or the light guides 118. However, these are just someexamples of modes of formation of the discontinuities 178, and thediscontinuities 178 may be formed by any mode of operation.

As also shown in FIG. 8 and discussed above, the liner layer 154 mayinclude discontinuities 179 that extend therethrough and would allow asolution or liquid to flow therethrough. The discontinuities 179 of theliner layer 154 may be relatively small internal discontinuities, pores,cracks or the like. The discontinuities 179 of the liner layer 154 maybe produced during the manufacturing stage of the liner layer 154 or thedevice 104, and/or during use of the device 104, for example. Thediscontinuities 179 of the liner layer 154 may be caused by differingthermal expansion coefficients of material of the liner 154 and otherportions of the device 104, for example. As another example, thediscontinuities 179 of the liner layer 154 may be caused by formationprocess thereof. In some examples, the discontinuities 179 of the linerlayer 154 may resulting from a liquid or solution interacting with theliner layer 154 and attacking, corroding or otherwise deteriorating theliner layer 154 (and thereby allow the liquid or solution to passthrough). However, these are just some examples of causes of thediscontinuities 179 of the liner layer 154, any the discontinuities 179may be formed by any mode of operation. In some examples, the linerlayer 154 may be comprised of a material that is chemically reactivewith reaction solution such that the reaction solution would etchthrough the liner layer 154 (and, ultimately, deteriorate the circuitry146). In some such embodiment, the liner layer 154 may or may not bevoid of the discontinuities 179.

When the discontinuities 178 are present and the reaction solution 170(or any other liquid or solution) is introduced onto the reactionstructure 126 (e.g., provided over the detection surface 112 and withinthe reaction recesses 108), the reaction solution 170 (or other liquidor solution) may be able to flow, wick, penetrate or otherwise travelwithin/through the discontinuities 178 or otherwise through the reactionstructure 126, and potentially through the filter material 116 of thelight guides 118, as shown in FIG. 8 . Further, as also shown in FIG. 8, if the protection layer 130 is not present, the discontinuities 179 ofthe liner layer 154 would allow such penetrated reaction solution 170(or other liquid or solution) to continue to travel through thedetection device 104 to the dielectric material 142 and, ultimately,interact with the circuitry 146. In another example, the penetratedreaction solution 170 (or other liquid or solution) may chemically reactwith the liner layer 154 and etch therethrough, and continue to travelthrough the detection device 104 to the dielectric material 142 and,ultimately, interact with the circuitry 146. As noted above, thereaction solution 170 may be relatively highly acidic (e.g., pH equal toor less than about 5) or relatively highly basic (e.g., pH equal to orgreater than about 8), and the liner layer 154 may comprise SiN which isrelatively easily etched by such a reaction solution. As also notedabove, the reaction solution 170 (or other liquid or solution) maydeteriorate or otherwise render the circuitry 146 in operable or lesseffective the conductive and/or metal portions of the circuitry 146. Forexample, the reaction solution 170 may chemically react and oxidize theconductive and/or metal portions of the circuitry 146.

However, as shown in FIG. 8 , the protection layer 130 may be configuredsuch that it forms a solid continuous barrier layer (without voids,cracks or other discontinuities) that prevents any reaction solution 170that penetrates through the reaction structure 126, and potentiallythrough the filter material 116 of the light guides 118, via thediscontinuities 178 or otherwise from interacting with the circuitry 146of the device 104. Further the protection layer 130 may be configuredsuch that it is chemically inert with respect to the reaction solutionsuch that the reaction solution (which may include a relatively highacidity or relatively high basicity, as described above) does not etchthe protection layer 130, or etches less than about one (1) angstrom (A)of the thickness of the protection layer 130 per hour at about 100degrees Celsius and at about atmospheric pressure, when the reactionsolution is in contact with the protection layer 130. In this way,although the discontinuities 179 or other pathways through the reactionstructure 126 and/or the discontinuities 179 or other pathways throughthe filter material 116 may be present, the protection layer 130prevents the reaction solution 170 from flowing to/through thediscontinuities 179 of the liner layer 154 and, ultimately, interactingwith (and thereby deteriorating) the device circuitry 146. As notedabove, the method of formation, thickness and material of the protectionlayer 130 may be configured, independently or in consideration of eachother, so that the protection layer 130 is void of any discontinuitiesthat would allow any solution or liquid (e.g., the reaction solution)from passing therethrough, and the protection layer 130 is chemicallyinert with respect to the reaction solution such that protection layer130 is etch resistant (by the reaction solution).

FIGS. 9-13 illustrates an example of a method 200 of manufacturing alight detection device, such as the light detection device 104 of FIGS.1-8 described. Therefore, like reference numerals preceded with “2,” asopposed to “1,” are used to indicate like components, aspects,functions, processes or functions, and the description above directed tothereto equally applies, and is not repeated for brevity and claritypurposes. The method 200, for example, may employ structures or aspectsof various examples (e.g., systems and/or methods) discussed herein. Invarious examples, certain steps may be omitted or added, certain stepsmay be combined, certain steps may be performed simultaneously, certainsteps may be performed concurrently, certain steps may be split intomultiple steps, certain steps may be performed in a different order, orcertain steps or series of steps may be re-performed in an iterativefashion.

As shown in FIGS. 9 and 10 , the method 200 of forming a device 204 mayinclude forming (at 270 of FIG. 9 ) a plurality (e.g., an array) oftrenches 280 within a device base 225. The plurality of trenches mayextend from an outer/external top surface of the device base 225 andtoward at least one corresponding light sensor 240 (through thethickness of the device base 225). As discussed above, the device base225 may include an array of light sensors 240 and device circuitry 246electrically coupled to the light sensors 240 that transmit data signalsbased on photons detected by the light sensors 240. The device base 225may be provided or obtained via any process. For example, the method 200may include obtaining the device base 225 in a preassembled orpremanufactured state, or include forming or manufacturing the devicebase 225 prior to forming 270 the plurality of trenches 280.

As discussed above, the device base 225 may be manufactured usingintegrated circuit manufacturing technologies, such as CMOSmanufacturing technologies. For example, the device base 225 may includeseveral substrate layers (e.g., dielectric material layers 242) withdifferent modified features (e.g., metallic elements) embedded thereinthat form the device circuitry 246. The plurality of trenches 280 may beformed in the substrate layers (e.g., in the dielectric material layers242) to correspond to portions of the device base 225 that will include,after the method 200, the light guides 218. While only one trench 280 isdepicted in FIG. 10 , the device base 225 may include an array of lightguides 218 as described above, and therefore an array of trenches 280may be formed.

As shown in FIG. 10 , the trenches 280 may extend through openings inthe first shield layer 250 and/or second shield layer 252, and throughthe dielectric material 242 toward at least one corresponding lightsensor 240. As shown in FIG. 10 , interior surfaces of the device base225, such as the dielectric material 242 thereof, may define thetrenches 280 for the formation of the light guides 218 therein. Thetrenches 280 may extend to the second liner layer 255 that extendsthrough the dielectric material 242. In this way, the second liner layer255 may form the bottom of the trenches 280. As also shown in FIG. 10 ,other openings in the first shield layer 250 and/or second shield layer252 may be formed in the interstitial areas 213 of the device base 225.

The trenches 280 may be formed by any process(es) or technique(s) thatremoves the portions of the dielectric material 242 (and potentiallyportions of the first shield layer 250 and/or second shield layer 252).For example, the trenches 280 may be formed by one or more selectiveetching processes or reactive ion etching process. In one example, thetrenches 280 may be formed by applying at least one mask (not shown) tothe device base 225 and removing material (e.g., through etching) of theportions of the dielectric material 242 (and potentially portions of thefirst shield layer 250 and/or second shield layer 252).

As shown in FIGS. 9 and 11 , after formation of the plurality oftrenches 280, the method 200 may include depositing (at 272 of FIG. 9 )the first liner layer 254 over the top surface of the device base 225and within the plurality of trenches 280. In some examples, the firstliner layer 254 may be formed over the sidewalls of the plurality oftrenches 280 and not over the second liner layer 255 at the bottom ofthe trenches 280. In some other examples, the first liner layer 254 maybe formed over the second liner layer 255 at the bottom of the trenches280, but then subsequently removed. The first liner layer 254 may bedeposited over the second shield layer 252 on the top surface of thedevice base 225, and potentially over any openings in the openings inthe first shield layer 250 and/or second shield layer 252 ininterstitial areas 213 of the device base 225 such that the secondshield layer 252 extends over the dielectric material 242 in suchopenings, as shown in FIG. 11 .

The first liner layer 254 may be formed by any process(es) ortechnique(s). For example, the first liner layer 254 may be formed by atleast one chemical deposition process (e.g., plating, chemical vapordeposition (CVD), plasma enhanced CVD (PECVD), or atomic layerdeposition (ALD), for example), a physical deposition process, a growthmode, epitaxy, or a combination thereof. In some examples, the firstliner layer 254 may be formed conformally over the surface of the devicebase 225 and within the trenches 280 (e.g., over the side walls and,potentially, the bottom surface of the trenches 280). The first linerlayer 254 may comprise a substantially constant thickness, or thethickness may vary. As discussed above, the first liner layer 254(and/or potentially the second liner layer 255) may comprisediscontinuities (upon formation and/or after use of the device 204) thatextend therethrough and allow a solution or liquid to flow therethrough(see FIG. 8 ). As also described above, the first liner layer 254 maychemically react with the reaction solution (which may be relativelyhighly acidic or basic/alkaline) such that the reaction solution etchestherethrough.

After formation of the first liner layer 254 on the device base 225 (andwithin the trenches 280), the first liner layer 254 may be furtherprocessed. For example, at least the portion of the first liner layer254 extending over the top surface of the device base 225 (i.e., theinterstitial areas 213 of the first liner layer 254) may be processed toflatten/planarize, smooth and/or otherwise improve the surfacetopography thereof. In some such examples, at least the portion of thefirst liner layer 254 extending over the top surface of the device base225 (i.e., the interstitial areas 213 of the first liner layer 254) maybe etched and/or polished (e.g., chemical and/or mechanicalpolishing/planarization) to planarize the outer surface of the firstliner layer 254.

As shown in FIGS. 9 and 12 , the method 200 may include depositing (at274 of FIG. 9 ) the protection layer 230 over the device base 225 suchthat it extends within the plurality of trenches 280. In some example,the method 200 may include depositing (at 274 of FIG. 9 ) the protectionlayer 230 over the device base 225 such that it extends within theplurality of trenches 280 and over the top surface of the device base225. In some examples, the protection layer 230 may be formed over thesidewalls of the plurality of trenches 280 and the bottom of thetrenches 280. The protection layer 230 may be formed over the firstliner layer 254 and the second liner layer 255.

The protection layer 230 may be formed by any process(es) ortechnique(s). For example, the protection layer 230 may be formed by atleast one chemical deposition process (e.g., plating, chemical vapordeposition (CVD), plasma enhanced CVD (PECVD), or atomic layerdeposition (ALD), for example), a physical deposition process, a growthmode, epitaxy, or a combination thereof. In some examples, theprotection layer 230 may be formed conformally over the surface of thedevice base 225 and within the trenches 280 (e.g., over the side wallsand, potentially, the bottom surface of the trenches 280). Theprotection layer 230 may comprise a substantially constant thickness, orthe thickness may vary. As discussed above, the protection layer 230 maybe formed such that it is void (upon formation and/or after use of thedevice 204) of any discontinuities that extend therethrough and wouldallow a solution or liquid to flow therethrough (see FIG. 8 ). Thethickness, material and/or formation process(es) of the protection layer230 may be configured so that the protection layer 230 is a liquidimpervious barrier layer. For example, any process that forms theprotection layer 230 as a robust, highly densified layer with a lowdefect density may be utilized. In some particular examples, theprotection layer 230 is formed via an atomic layer deposition (ALD)process or a high-density plasma chemical vapor deposition (CVD)process, for example. The protection layer 230 may thereby be a liquidimpervious barrier that prevents and liquid or solution, such as thereaction solution, from interacting with the device circuitry 246 inthis device layers of the device base 225.

As also discussed above, the protection layer 230 may be formed suchthat it is chemically inert with respect to the reaction solution suchthat the reaction solution (which may include a relatively high acidityor relatively high basicity, as described above) does not etch theprotection layer 230, or etches less than about one (1) angstrom (A) ofthe thickness of the protection layer 230 per hour at about 100 degreesCelsius and at about atmospheric pressure, when the reaction solution isin contact with the protection layer 230. For example, the compositionof the protection layer 230 may not chemically react, or chemicallyreacts to only a relatively small degree, with the composition of thereaction solution (which may include a relatively high acidity orrelatively high basicity) such that the reaction solution does not etchthe protection layer 230 or etches less than about one (1) angstrom (A)of the thickness of the protection layer 230 per hour at about 100degrees Celsius and at about atmospheric pressure when the reactionsolution is in contact with the protection layer 230. The protectionlayer 230 may thereby comprise an etch resistant layer with respect tothe reaction solution (which may include a pH equal to or less thanabout 5 or a pH equal to or greater than about 8, for example) toprevent the reaction solution from penetrating therethrough (over time)and, ultimately, interacting with and corroding or otherwise interferingwith the functioning of the device circuitry 246. The protection layer230 may thereby be formed to prevent a liquid or solution (such as thereaction solution) that may penetrate through the reaction structure 226to the protection layer 230, or through the reaction structure 226 andthe filter material 216 of a light guide 218 to the protection layer230, from interacting with the device circuitry 246 (and the liner layer254 (if provided) and the dielectric material 242).

As shown in FIGS. 9 and 13 , after formation of the protection layer230, the method 200 may include filling (at 276 of FIG. 9 ) theplurality of lined trenches 280 with at least one filter material 216 toform the plurality of light guides 218. As discussed above, the at leastone filter material 216 may filter light of a first wavelength (e.g.,excitation light) and permits light of a second wavelength (e.g.,emitted light from reaction sites) to pass therethrough to at least onecorresponding light sensor 240. In some examples, the amount of thefilter material 216 applied to the device base 225 may exceed theavailable volume within the lined trenches 280. As such, the filtermaterial 216 may overflow the lined trenches 280 and extend along thetop of the device base 225, such as over the first liner layer 254. Inalternative examples, the filling operation 276 may include selectivelyfilling each lined trench 280 such that the filter material 216 does notclear/overflow the trench 280 (i.e., extend over the top of the devicebase 225).

In some examples, filling (at 276 of FIG. 9 ) the filter material 216may include pressing (e.g., using a squeegee-like component) the filtermaterial 216 into the lined trenches 280. Optionally, the method 200 mayalso include removing the filter material 216 from the protection layer230 and, in some cases, portions of the filter material 216 within thelight guides 218. The filter material 216 may be removed from within thelight guides 218 so that the opening 258 of the light guides 218 islocated at a depth below the protection layer 230, as shown in FIG. 13 .Different processes may be implemented for removing one or more portionsof the filter material 216. For example, a removal operation may includeat least one of etching the portions of the filter material 216 orchemically polishing the portions of the filter material 216.

As also shown in FIGS. 9 and 13 , after formation of the protectionlayer 230 on the device base 225 (and within the trenches 280), theprotection layer 230 may be further processed. For example, at least theportion of the protection layer 230 extending over the top surface ofthe device base 225 (i.e., the interstitial areas 213 of the protectionlayer 230) may be processed to flatten/planarize, smooth and/orotherwise improve the surface topography thereof. In some such examples,at least the portion of the protection layer 230 extending over the topsurface of the device base 225 (i.e., the interstitial areas 213 of theprotection layer 230) may be etched and/or polished (e.g., chemicaland/or mechanical polishing/planarization) to planarize the outersurface of the protection layer 230.

After formation of the light guides 218 via the filter material 216, themethod 200 may include forming (at 278 of FIG. 9 ) a reaction structureover the plurality of light guides 218 and over the protection layer 230on the top surface of the device base 225 (see FIGS. 3 and 4 ). Asdiscussed above, the reaction structure provided over the plurality oflight guides 218 and over the protection layer 230 on the top surface ofthe device base 225 may include a plurality of reaction recesses eachcorresponding to at least one light guide for containing at least onereaction site and a reaction solution. In some examples, reactionsolution with a pH of less than or equal to about 5 or a pH of greaterthan or equal to about 8 is provided over the reaction structure to formreaction sites thereon. The reaction sites may generate light emissionsin response to incident excitation light after treatment with thereaction solution. For example, the reaction solution may initiate areaction and/or form a reaction product at the reaction sites thatgenerates light emissions in response to the excitation light. As alsodiscussed above, the reaction structure may comprise a plurality oflayers. As such, forming (at 278 of FIG. 9 ) the reaction structure mayinclude forming a plurality of layers over the plurality of light guides218 and over the protection layer 230 on the top surface of the devicebase 225 (see FIGS. 3 and 4 ). The reaction structure may be formed byany process(es) or technique(s).

The protection layer 230 may thereby form an underlying support to thereaction structure. As discussed above, the planarized top surface ofthe protection layer 230 may thereby minimize surface topographymodulation induced in the detector surface of the reaction structure,particularly to the interstitial areas 213 of the detector surface. Inparticular examples, the processed protection layer 230 may result in aplanar and/or smooth surface to the interstitial areas 213 of thedetector surface of the reaction structure and prevent the reactionsolution or any other biological or chemical substances from remainingthereon and/or prevent pad hopping errors. The flatness of theinterstitial areas 213 of the detector surface, provided at least inpart by the processed underlying protection layer 230, may enhance therobustness of the detection device 204 as compared to examples that arevoid of the processed protection layer 230.

Optionally, the method 200 may include providing at least one reactionsites in at least one reaction recess of the formed reaction structureby introducing a reaction solution with a pH of less than or equal toabout 5 or a pH greater than or equal to about 8 over the reactionstructure and/or mounting a flow cell to the device 204 (see FIG. 1 )that provides a reaction solution with a pH of less than or equal toabout 5 or a pH greater than or equal to about 8 over the reactionstructure. Providing the reaction sites may occur prior to or after theflow cell is coupled to the device 204. The reaction sites may bepositioned at a predetermined pattern along the reaction recesses. Thereaction sites may correspond (e.g., one site to one light sensor, onesite to multiple light sensors, or multiple sites to one light sensor)in a predetermined manner. In other examples, the reaction sites may berandomly formed along the reaction recesses. As described herein, thereaction sites may include biological or chemical substances immobilizedto the detector surface within the reaction recesses. The biological orchemical substances may be configured to emit light signals in responseto excitation light. The at least one reaction site may thereby generatelight emissions in response to incident excitation light only aftertreatment with the reaction solution. For example, the reaction solutionmay initiate a reaction and/or form a reaction product at the at leastone reaction site that generates light emissions in response to theexcitation light. In particular examples, the reaction sites includeclusters or colonies of biomolecules (e.g., oligonucleotides) that areimmobilized on the detector surface within the reaction recesses.

It is to be understood that the above description is intended to beillustrative, and not restrictive. For example, the above-describedexamples (and/or aspects thereof) may be used in combination with eachother. In addition, many modifications may be made to adapt a particularsituation or material to the teachings of the various examples withoutdeparting from their scope. While dimensions and types of materials maybe described herein, they are intended to define parameters of some ofthe various examples, and they are by no means limiting to all examplesand are merely exemplary. Many other examples will be apparent to thoseof skill in the art upon reviewing the above description. The scope ofthe various examples should, therefore, be determined with reference tothe appended claims, along with the full scope of equivalents to whichsuch claims are entitled.

In the appended claims, the terms “including” and “in which” are used asthe plain-English equivalents of the respective terms “comprising” and“wherein.” Moreover, in the following claims, the terms “first,”“second,” and “third,” etc. are used merely as referee labels, and arenot intended to impose numerical, structural or other requirements ontheir objects. Forms of term “based on” herein encompass relationshipswhere an element is partially based on as well as relationships where anelement is entirely based on. Forms of the term “defined” encompassrelationships where an element is partially defined as well asrelationships where an element is entirely defined. Further, thelimitations of the following claims are not written inmeans-plus-function format and are not intended to be interpreted basedon 35 U.S.C. § 112, sixth paragraph, unless and until such claimlimitations expressly use the phrase “means for” followed by a statementof function void of further structure. It is to be understood that notnecessarily all such objects or advantages described above may beachieved in accordance with any particular example. Thus, for example,those skilled in the art will recognize that the devices, systems andmethods described herein may be embodied or carried out in a manner thatachieves or optimizes one advantage or group of advantages as taughtherein without necessarily achieving other objects or advantages as maybe taught or suggested herein.

While the disclosure has been described in detail in connection withonly a limited number of examples, it should be readily understood thatthe disclosure is not limited to such disclosed examples. Rather, thisdisclosure can be modified to incorporate any number of variations,alterations, substitutions or equivalent arrangements not heretoforedescribed, but which are commensurate with the spirit and scope of thedisclosure. Additionally, while various examples have been described, itis to be understood that aspects of the disclosure may include only oneexample or some of the described examples. Also, while some examples aredescribed as having a certain number of elements, it will be understoodthat the examples can be practiced with less than or greater than thecertain number of elements.

It should be appreciated that all combinations of the foregoing conceptsand additional concepts discussed in greater detail below (provided suchconcepts are not mutually inconsistent) are contemplated as being partof the inventive subject matter disclosed herein. In particular, allcombinations of claimed subject matter appearing at the end of thisdisclosure are contemplated as being part of the inventive subjectmatter disclosed herein.

What is claimed is:
 1. A device, comprising: a reaction structure comprising a plurality of reaction sites; and a device base positioned beneath the reaction structure, comprising: a plurality of light sensors; device circuitry electrically coupled to the light sensors to transmit data signals based on photons detected by the light sensors, a plurality of light guides with input regions that receive excitation light and light emissions from at least one of the plurality of reaction sites, the light guides extending into the device base from the input regions toward at least one light sensor of the plurality of light sensors, and said light guides comprising at least one filter material that filters at least some of the excitation light and permits at least some of the light emissions to pass to the at least one light sensor; a protection layer extending about each light guide, where the protection layer is chemically inert with respect to a reaction solution that passes over the reaction structure; and a shield layer extending between adjacent input regions to block the excitation light and light emissions incident on the shield layer.
 2. The device of claim 1, wherein the protection layer abuts the plurality of light guides within the device base.
 3. The device of claim 1, further comprising a liner layer, where the liner layer extends over the device base and about side surfaces of each light guide and is positioned between each light guide and the device circuitry.
 4. The device of claim 1, wherein the protection layer further extends between a top surface of the device base and interstitial areas of the reaction structure extending about the reaction sites.
 5. The device of claim 1, wherein the device base further comprises a second shield layer that extends over the shield layer, where the second shield layer comprises anti-reflective material.
 6. The device of claim 1, wherein the protection layer comprises silicon dioxide, a metal oxide, a metal nitride or a combination thereof.
 7. The device of claim 1, wherein the protection layer comprises silicon dioxide, silicon oxynitride, silicon monoxide, silicon carbide, silicon oxycarbide, silicon nitrocarbide, metal oxide, metal nitride or a combination thereof.
 8. The device of claim 1, wherein the pH of the reaction solution is greater than or equal to about
 8. 9. The device of claim 1, wherein the pH of the reaction solution is less than or equal to about 5, and wherein the protection layer comprises silicon carbide, silicon oxycarbide, silicon nitrocarbide, a metal oxide, a metal nitride or a combination thereof.
 10. The device of claim 3, wherein the liner layer comprises silicon nitride.
 11. The device of claim 1, wherein the protection layer is a liquid impervious barrier layer.
 12. The device of claim 1, wherein the device circuitry comprises interconnected conductive elements, and the protection layer prevents the reaction solution from oxidizing the conductive elements.
 13. The device of claim 1, wherein the thickness of the protection layer is within the range of nanometers to 100 nanometers.
 14. The device of claim 1, wherein the reaction structure further comprises a plurality of reaction recesses, where at least one reaction site of the plurality of reaction sites is immobilized to the reaction structure within each of the plurality of reaction recesses.
 15. The device of claim 14, wherein at least one of the plurality of reaction sites comprises at least one analyte, the device further comprising the reaction solution, the reaction solution forms a reaction product with the at least one analyte that generates light emissions in response to the incident excitation light, wherein the reaction solution comprises at least one fluorescently-labeled molecule.
 16. The device of claim 1, wherein the device circuitry of the device base forms complementary metal-oxide semiconductor (CMOS) circuits.
 17. A biosensor, comprising: the device of claim 1; and a flow cell mounted to the device comprising the reaction solution and at least one flow channel that is in fluid communication with the plurality of reaction sites of the reaction structure to direct the reaction solution thereto.
 18. A method, comprising: delivering a reaction solution to a plurality of reaction sites of a device, where the device comprises: a reaction structure comprising the plurality of reaction sites; and a device base positioned beneath the reaction structure, comprising: a plurality of light sensors; device circuitry electrically coupled to the light sensors to transmit data signals based on photons detected by the light sensors, a plurality of light guides with input regions that receive excitation light and light emissions from at least one of the plurality of reaction sites, the light guides extending into the device base from the input regions toward at least one light sensor of the plurality of light sensors, and said light guides comprising at least one filter material that filters at least some of the excitation light and permits at least some of the light emissions to pass to the at least one light sensor; a protection layer extending about each light guide, where the protection layer is chemically inert with respect to the reaction solution that passes over the reaction structure; and a shield layer extending between adjacent input regions to block the excitation light and light emissions incident on the shield layer; and detecting the light emissions by the light sensors.
 19. The method of claim 18, further comprising illuminating the reaction sites with the excitation light using an excitation light source.
 20. The method of claim 18, wherein the reaction solution comprises four types of nucleotides. 